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CombiMatrix Study Shows Arrays Outperform Standard Karyotyping in Thousands of Miscarriage Analyses

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NEW YORK (GenomeWeb) — CombiMatrix presented data this week showing that chromosomal microarray analysis of more than 4,000 miscarriage analyses yielded a successful result over 85 percent of the time.

By comparison, standard karyotyping methods are successful at analyzing miscarriage tissue only about 60 percent of the time, according to Trilochan Sahoo, director of cytogenetics for CombiMatrix, who presented the company's results at the annual meeting of the American Society of Human Genetics.

The data, from 4,652 total samples, represent several years' worth of products of conception (POC) testing by the company using a progression of different array technologies. Overall, during the study period, CombiMatrix reported array-based testing yielded a successful result for more than 85 percent of cases.

The New York State Department of Health conditionally approved CombiMatrix's CombiSNP Array for Pregnancy Loss for testing of fresh and formalin-fixed, paraffin-embedded patient samples in July.

CombiMatrix has announced a number of partnerships over the last year or so to offer CMA for miscarriage, including deals with American Pathology Partners, ProPath, and Manhattan Laboratories.

Sahoo told BioArray News that several small studies have shown in recent years that microarrays outperform traditional cytogenetics methods in analyzing the challenging tissues that can characterize pregnancy loss. In its study, CombiMatrix set out to replicate and build on these smaller efforts with a much larger, long-term analysis.

In his presentation, Sahoo reported on the results of the company's testing of 4,652 consecutive specimens over several years, including 3,767 fresh POC samples and 885 FFPE samples. According to the data about 86 percent of the analyses of fresh samples yielded a successful result, and about 75 percent of the FFPE samples also could be successfully analyzed.

During the study period, CombiMatrix used three different chromosomal microarray platforms — BAC-aCGH, oligo-aCGH, and most recently a SNP array, the Illumina CytoSNP 850K, which underlies its current commercial offerings. Of the three platforms, the SNP array, which was used for about 70 percent of the total study cohort, had the highest abnormality detection rate at about 54 percent, Sahoo reported. The SNP platform also identified cases with whole genome or multiple regions of allelic homozygosity in addition to chromosomal imbalances, the researchers reported.

Though microarrays require equipment and expertise beyond traditional karyotype analyses, Sahoo said that the company's data, coupled with earlier smaller studies, demonstrate without a doubt that there is added value in array-based POC testing. This is not only because of its higher diagnostic yield, but also because the more advanced modern SNP-based arrays like the Illumina arrays CombiMatrix uses allow for the detection of complex abnormalities previous methods could not pick out.

"We can identify a whole spectrum of different abnormalities, some of which were unrecognizable before now," Sahoo said. "For example, we are finding things like unbalanced rearrangements with high sensitivity and specificity, and that likely also contributes significantly to our high success rate," he added.

Also important, Sahoo said, was that the study demonstrated that array-based testing also performed well on FFPE tissue. In the miscarriage or pregnancy loss analysis space, tissue can often be sent fresh for testing, but it is also frequently first passed through the pathology lab, and then moved forward for testing by companies like CombiMatrix after it has been preserved and fixed in a paraffin block.

"Even for those FFPE specimens, which are known to be challenging, we have achieved close to 75 percent success rate," Sahoo said.

The group is now planning to publish its study fully in the scientific literature. They are also looking into their results more closely as they pertain to the frequency of different types of chromosomal abnormalities in the landscape of pregnancy loss.

Miscarriage analysis makes up a significant portion, though not a majority of ComibiMatrix's testing, Sahoo said.

The company has benefitted over the last year from new guidelines released in 2013 by the American Congress of Obstetricians and Gynecologists and the Society of Maternal Fetal-Medicine recommending prenatal chromosomal microarray analysis as the preferred methodology to identify the cause of death in stillbirths.

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